Nucleic Acids Research

Articles:

Greg L. Olsen, Thomas E. Edwards, Pritilekha Deka, Gabriele Varani, Snorri Th. Sigurdsson, and Gary P. Drobny

Monitoring tat peptide binding to TAR RNA by solid-state ³¹P–¹⁹F REDOR NMR
Nucl. Acids Res. 2005 33: 3447-3454; doi:10.1093/nar/gki626 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thomas S. Price, Regina Regan, Richard Mott, Åsa Hedman, Ben Honey, Rachael J. Daniels, Lee Smith, Andy Greenfield, Ana Tiganescu, Veronica Buckle, Nicki Ventress, Helena Ayyub, Anita Salhan, Susana Pedraza-Diaz, John Broxholme, Jiannis Ragoussis, Douglas R. Higgs, Jonathan Flint, and Samantha J. L. Knight

SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data
Nucl. Acids Res. 2005 33: 3455-3464; doi:10.1093/nar/gki643 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tomonori Yoshida, Tsuyoshi Ohkumo, Shoko Ishibashi, and Kunio Yasuda

The 5'-AT-rich half-site of Maf recognition element: a functional target for bZIP transcription factor Maf
Nucl. Acids Res. 2005 33: 3465-3478; doi:10.1093/nar/gki653 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jiang Qian, Noriko Esumi, Yangjian Chen, Qingliang Wang, Itay Chowers, and Donald J. Zack

Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation
Nucl. Acids Res. 2005 33: 3479-3491; doi:10.1093/nar/gki658 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jennifer M. Kalish, Michael M. Seidman, Daniel L. Weeks, and Peter M. Glazer

Triplex-induced recombination and repair in the pyrimidine motif
Nucl. Acids Res. 2005 33: 3492-3502; doi:10.1093/nar/gki659 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Elizabeth D. Pratico, Yangming Wang, and Scott K. Silverman

A deoxyribozyme that synthesizes 2',5'-branched RNA with any branch-site nucleotide
Nucl. Acids Res. 2005 33: 3503-3512; doi:10.1093/nar/gki656 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jacob A. Theruvathu, Pawel Jaruga, Raghu G. Nath, Miral Dizdaroglu, and P. J. Brooks

Polyamines stimulate the formation of mutagenic 1,N²-propanodeoxyguanosine adducts from acetaldehyde
Nucl. Acids Res. 2005 33: 3513-3520; doi:10.1093/nar/gki661 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anje Sporbert, Petra Domaing, Heinrich Leonhardt, and M. Cristina Cardoso

PCNA acts as a stationary loading platform for transiently interacting Okazaki fragment maturation proteins
Nucl. Acids Res. 2005 33: 3521-3528; doi:10.1093/nar/gki665 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Natalia Ivanova, Michael Y. Pavlov, Elli Bouakaz, Måns Ehrenberg, and Lovisa Holmberg Schiavone

Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA
Nucl. Acids Res. 2005 33: 3529-3539; doi:10.1093/nar/gki666 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Masatoshi Jinnin, Hironobu Ihn, Yoshihiro Mimura, Yoshihide Asano, Kenichi Yamane, and Kunihiko Tamaki

Matrix metalloproteinase-1 up-regulation by hepatocyte growth factor in human dermal fibroblasts via ERK signaling pathway involves Ets1 and Fli1
Nucl. Acids Res. 2005 33: 3540-3549; doi:10.1093/nar/gki648 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andrzej Grajkowski, Joao Pedras-Vasconcelos, Vivian Wang, Cristina Ausín, Sonja Hess, Daniela Verthelyi, and Serge L. Beaucage

Thermolytic CpG-containing DNA oligonucleotides as potential immunotherapeutic prodrugs
Nucl. Acids Res. 2005 33: 3550-3560; doi:10.1093/nar/gki657 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ann Båvner, Jason Matthews, Sabyasachi Sanyal, Jan-Åke Gustafsson, and Eckardt Treuter

EID3 is a novel EID family member and an inhibitor of CBP-dependent co-activation
Nucl. Acids Res. 2005 33: 3561-3569; doi:10.1093/nar/gki667 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jin-Wu Nam, Ki-Roo Shin, Jinju Han, Yoontae Lee, V. Narry Kim, and Byoung-Tak Zhang

Human microRNA prediction through a probabilistic co-learning model of sequence and structure
Nucl. Acids Res. 2005 33: 3570-3581; doi:10.1093/nar/gki668 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Wagane J. Benga, Sylvie Grandemange, George V. Shpakovski, Elena K. Shematorova, Claude Kedinger, and Marc Vigneron

Distinct regions of RPB11 are required for heterodimerization with RPB3 in human and yeast RNA polymerase II
Nucl. Acids Res. 2005 33: 3582-3590; doi:10.1093/nar/gki672 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Melissa A. Calmann, James E. Evans, and M. G. Marinus

MutS inhibits RecA-mediated strand transfer with methylated DNA substrates
Nucl. Acids Res. 2005 33: 3591-3597; doi:10.1093/nar/gki673 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lisa N. Kinch, Krzysztof Ginalski, Leszek Rychlewski, and Nick V. Grishin

Identification of novel restriction endonuclease-like fold families among hypothetical proteins
Nucl. Acids Res. 2005 33: 3598-3605; doi:10.1093/nar/gki676 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rui Hao, Ming-Wei Zhao, Zhan-Xi Hao, Yong-Neng Yao, and En-Duo Wang

A T-stem slip in human mitochondrial tRNA^Leu(CUN) governs its charging capacity
Nucl. Acids Res. 2005 33: 3606-3613; doi:10.1093/nar/gki677 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andrew F. Neuwald

Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases
Nucl. Acids Res. 2005 33: 3614-3628; doi:10.1093/nar/gki674 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Iaroslav Ispolatov, Anton Yuryev, Ilya Mazo, and Sergei Maslov

Binding properties and evolution of homodimers in protein–protein interaction networks
Nucl. Acids Res. 2005 33: 3629-3635; doi:10.1093/nar/gki678 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Tingyi Wen, Irina A. Oussenko, Olivier Pellegrini, David H. Bechhofer, and Ciarán Condon

Ribonuclease PH plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors in Bacillus subtilis
Nucl. Acids Res. 2005 33: 3636-3643; doi:10.1093/nar/gki675 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

John Gladitz, Kai Shen, Patricia Antalis, Fen Ze Hu, J. Christopher Post, and Garth D. Ehrlich

Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae
Nucl. Acids Res. 2005 33: 3644-3658; doi:10.1093/nar/gki670 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xinhua Guo, Michael F. Bruist, Darryl L. Davis, and Catherine M. Bentzley

Secondary structural characterization of oligonucleotide strands using electrospray ionization mass spectrometry
Nucl. Acids Res. 2005 33: 3659-3666; doi:10.1093/nar/gki671 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael J. Volles and Peter T. Lansbury, Jr

A computer program for the estimation of protein and nucleic acid sequence diversity in random point mutagenesis libraries
Nucl. Acids Res. 2005 33: 3667-3677; doi:10.1093/nar/gki669 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Colin P. Guy and Edward L. Bolt

Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands
Nucl. Acids Res. 2005 33: 3678-3690; doi:10.1093/nar/gki685 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Primoz Sket, Martin Crnugelj, and Janez Plavec

Identification of mixed di-cation forms of G-quadruplex in solution
Nucl. Acids Res. 2005 33: 3691-3697; doi:10.1093/nar/gki690 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Corrigendum:

Quan Du, Håkan Thonberg, Jue Wang, Claes Wahlestedt, and Zicai Liang

A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites
Nucl. Acids Res. 2005 33: 3698; doi:10.1093/nar/gki647 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Zhiwen Tang, Kemin Wang, Weihong Tan, Changbei Ma, Jun Li, Lingfeng Liu, Qiuping Guo, and Xiangxian Meng

Real-time investigation of nucleic acids phosphorylation process using molecular beacons
Nucl. Acids Res. 2005 33: e97; doi:10.1093/nar/gni096 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Aurélien Crut, Bénédicte Géron-Landre, Isabelle Bonnet, Stéphane Bonneau, Pierre Desbiolles, and Christophe Escudé

Detection of single DNA molecules by multicolor quantum-dot end-labeling
Nucl. Acids Res. 2005 33: e98; doi:10.1093/nar/gni097 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ron M. McCullough, Charles R. Cantor, and Chunming Ding

High-throughput alternative splicing quantification by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Nucl. Acids Res. 2005 33: e99; doi:10.1093/nar/gni098 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gaëlle Rondeau, Michael McClelland, Toan Nguyen, Rosana Risques, Yipeng Wang, Martin Judex, Ann H. Cho, and John Welsh

Enhanced microarray performance using low complexity representations of the transcriptome
Nucl. Acids Res. 2005 33: e100; doi:10.1093/nar/gni095 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Benjamin Bockisch, Thomas Grunwald, Edzard Spillner, and Reinhard Bredehorst

Immobilized stem–loop structured probes as conformational switches for enzymatic detection of microbial 16S rRNA
Nucl. Acids Res. 2005 33: e101; doi:10.1093/nar/gni101 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xavier Coumoul, Vivek Shukla, Cuiling Li, Rui-Hong Wang, and Chu-Xia Deng

Conditional knockdown of Fgfr2 in mice using Cre-LoxP induced RNA interference
Nucl. Acids Res. 2005 33: e102; doi:10.1093/nar/gni100 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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